In a recent article a group of German and Canadian researchers presented the genome of Yersinia pestis as it has been extracted from burials of the London East Smithfield burial ground dated to 1348/49 (Bos et al. 2011). This site has been excavated by the Museum of London after it has been localised in 1986 (Grainger et al. 2008).

The article aims at the reconstruction of the ancient genome of Yersinia pestis, as this promises implications for the understanding of infectious diseases, as "genomic data from ancient microbes may help to elucidate mechanisms of pathogen evolution and adaptation for emerging and re-emerging infections".

The authors conclude:

1.) "Genetic architecture and phylogenetic analysis indicate that the ancient organism is ancestral to most extant strains and sits very close to the ancestral node of all Y. pestis commonly associated with human infection. Temporal estimates suggest that the Black Death of 1347–1351 was the main historical event responsible for the introduction and widespread dissemination of the ancestor to all currently circulating Y. pestis strains pathogenic to humans." The classic Black Death was quite different from previous epidemics. The authors refer to the Justinian plague "popularly assumed to have resulted from the same pathogen: our temporal estimates imply that the pandemic was either caused by a Y. pestis variant that is distinct from all currently circulating strains commonly associated with human infections, or it was another disease altogether."

2.) "Comparisons against modern genomes reveal no unique derived positions in the medieval organism, indicating that the perceived increased virulence of the disease during the Black Death may not have been due to bacterial phenotype. These findings support the notion that factors other than microbial genetics, such as environment, vector dynamics and host susceptibility, should be at the forefront of epidemiological discussions regarding emerging Y. pestis infections."

As I am not familiar with genetics I do not dare to give any comment on this argumentation itself. However as has been stated before (see Michelle Ziegler at Contagions) the article is lacking a historical perspective - and as a medieval archaeologist there are several points I want to highlight:

Concerning the history of the plague itself, there has been another genetic study some years ago, which identified Yersinia pestis-specific DNA during genetic investigation of a double inhumation, presumably a mother/child burial from Aschheim (Upper Bavaria, 6th century A.D.) (Wiechmann/ Grupe 2005). In this study the sequences of the "amplification products shared 100% identity with that of the modern Y. pestis pla sequence in GenBank, with the exception of one amplification product which revealed a single base substitution." Even if we do not have written evidence that the Justinian plague also occurred in Bavaria, this proof for the presence of Y. pestis in the second half of the 6th century A.D. is a strong argument that the Justinian plague has indeed been caused by Yersinia pestis.

This raises the question how the DNA of Y. pestis from Aschheim fits within the proposed evolution of Y. pestis shortly before the 14th centuries black death. The new study compared the East Smithfield DNA only with modern databases and lacks other historical data, which could verify their theory of a just recent evolution of Y. pestis.

Dealing with the circumstances of the 14th century Black Death the observation of just little changes in the Y. pestis DNA since the 14th century raises indeed the question, why the plague 1347ff. was that devastating, whereas the later ones were less virulent. Furthermore we have to ask why there has been no similar severe plague between the 6th and the 14th century.

If Y. pestis did not evolve in the last 650 years in a larger scale, this rises the question wether there may have been a human adaptation to the virus. And we should ask if there has been already an adaptation to an older variation of Y. pestis before? That's a question for medicine. A closer look and a more detailed comparison between the Aschheim and the Smithfield genom is urgently required.

To look at environmental factors, historical and archaeological data are crucial. However, despite a long lasting discussion about the late medieval crisis, it is very hard to depict its consequences for the environment and the daily life. Previous studies hinted to a period of late medieval deserted villages connected with the 14th century crisis. Besides an "agrarian crisis" especially the plague has often been thought to be responsible for the abandonment of rural settlements (Schreg 2011).

However many regional studies showed, that the process of late medieval settlement abandonment has been much more complex - and lasted over several generations. It is hardly possible to connect this process with one single event as the Black Death from 1347ff. Furthermore many palynological studies cases do not show any devastation and reforestation of land as it has been postulated.

Rodent's ecologyIt has been suggested, that the weakened condition of the human population, still suffering from the bad weather conditions and crop failures in the early 14th century was more prone to the plague. However, there may be an alternative explanation for the outbreak of the Black Death in the context of the late medieval crisis. New studies on the chain of infection of the plague assume a direct infection from rodents to humans. According to these studies the epidemiological chain of Y. pestis has to be completed by introducing soil as a kind of a reservoir (Drancourt et al. 2006, pp. 234f.). There should have been a high risk of human infection when the ecology of rodents has been disturbed.

Future research should ask for the role of the extreme weather of July 1342 causing St. Mary Magdalene's flood (Bork 2006, pp. 115ff.) and the plague some years later. The 14th century landscape was an open landscape with less forest than today and the introduction of the open field system managed with three field crop rotation some generations before made the landscape very vulnerable for soil erosion. Probably the open landscape even contributed to the weather extremes. Heating effects over large fields may have influenced local thunderstorms.

When 1342 heavy rains came over central Europe they destroyed the fields - only a few weeks before harvest. The grain was germinable at that time. As the fields were destroyed and grains were washed away and cereals were probably growing at many places in the open landscape in the following years. The resulting large food supply might have influenced the rodents' ecosystem much more severely than the destruction of their dens. May a grown rodent population have come in closer contact to humans?

But taking the hypothesis, that changes in rodents' ecology as a consequence were due to weather extremes which have probably been enhanced by land use practices, means to ask for anthropogenic impact on the spread of the plague. Therefore we need to have a closer look on the spread of the plague. Maps showing large coloured distributions may hide the more important regional scale. Much more detailed maps are needed, that show the break-out of the plague distinguishing between the regional and social environments, dealing very cautious by using the evidence of anti-Jewish pogroms as an indication for the plague. This kind of maps should be compared especially with the evidence of the 1342 St. Mary Magdalene's flood. Was there an anthropogenic factor in the early 14th century weather extremes and the distribution of the plague?What were the effects of the 1342 flood on the landscape? Do current evidences pass a critical evaluation? How was rodents' ecology affected by the St. Mary Magdalene's flood?If we want to verify this scenario, we also need a comparative approach looking for analogies. We need to ask whether there is a correlation between changes of the rural landscape, weather events, rodent's ecology and diseases to be observed in other historical situations. However, dealing with this hypothesis we need to take into account, that there may be other, historical i.e. factors, specific in time, space and cultural tradition. Urban archaeology gives us some indication that some towns suffered already in the early 14th century and that there may have been "social fallow" within the towns which also could have some effects on the population of rats and rodents. And we need to take into account the cultural behaviour of people.

Mutation of Yersinia pestis

However, despite there was an indigenous variant of Y. pestis present in Central Europe even before 1347, written sources show a spreading of the plague starting in the East and reaching Central Europe from the Mediterranean. Therefore it is unlikely that the plague crossed from rodents to humans in Central Europe as a result of the 1342 event and a consequently disturbed rodents' ecology. In addition, the new DNA study suggests that Y. pestis mutated just shortly before 1347. As stated before, we need to know the relationship of the Smithfield and the Aschheim Y.pestis genome. Is it possible that people were adapted to the old indigenous "Justinian" y.pestis, which got virulent when a new variant of the virus came to Europe via Crimea and the Mediterranean? In the Islamic world the Black Death was also present but it was less this catastrophic event. Was this just due to another cultural recognition of the disease? Hygiene but also the awareness, that antique historical sources, preserved in Arabic libraries, show that there have been similar diseases before, probably just caused a different reception of the Black Death. Or was the Black Death less virulent in the Eastern Mediterranean and Africa? What is the relation between the Aschheim and the London virus from a genetic point of view? When Naphy & Spicer neglected that the correct diagnosis of the plague has any importance for cultural history they were surely wrong. The chain of infection highly depends from ecological and cultural preconditions - and the genetic determination of variants of Y.pestis influences the historical interpretation.

There is much speculation at that point. ‒ There are many questions for a challenging interdisciplinary approach, if it succeeds to build up a team of researchers working very closely together and overcoming specific disciplinary traditional perspectives. However, it seems evident, that a more ecological and historical perspective has to be added to the genetic research if we want to understand the complex history of the plague and the "14th century's crisis".

A. Cunningham, Disease: Crisis or Transformation? In: T. Dahlerup/P. Ingesman (eds.), New approaches to the history of late medieval and early modern Europe. Selected proceedings of two international conferences at the Royal Danish Academy of Sciences and Letters in Copenhagen 1997 and 1999. Historisk-filosofiske meddelelser 104 (Copenhagen 2009) 365–396.

Working in archaeology is not to discover treasures and to disclose secrets! It's rather to learn about our past, our present and ourselves. This requires meticulous work in detail and the courage (and adequate methodology) to draw overall conclusions.